Genomes of rumen bacteria encode atypical pathways for fermenting hexoses to short‐chain fatty acids

Hackmann Timothy J.; Ngugi David Kamanda; Firkins Jeffrey L.; Tao Junyi

摘要

Summary >Bacteria have been thought to follow only a few well‐recognized biochemical pathways when fermenting glucose or other hexoses. These pathways have been chiseled in the stone of textbooks for decades, with most sources rendering them as they appear in the classic 1986 text by Gottschalk. Still, it is unclear how broadly these pathways apply, given that they were established and delineated biochemically with only a few model organisms. Here, we show that well‐recognized pathways often cannot explain fermentation products formed by bacteria. In the most extensive analysis of its kind, we reconstructed pathways for glucose fermentation from genomes of 48 species and subspecies of bacteria from one environment (the rumen). In total, 44% of these bacteria had atypical pathways, including several that are completely unprecedented for bacteria or any organism. In detail, 8% of bacteria had an atypical pathway for acetate formation; 21% of bacteria had an atypical pathway for propionate or succinate formation; 6% of?bacteria had an atypical pathway for butyrate formation and 33% of bacteria had an atypical or incomplete Embden–Meyerhof–Parnas pathway. This study shows that reconstruction of metabolic pathways – a common goal of omics studies – could be incorrect if well‐recognized pathways are used for reference. Furthermore, it calls for renewed efforts to delineate fermentation pathways biochemically. </abstract> </span> <span class="z_kbtn z_kbtnclass hoverxs" style="display: none;">展开▼</span> </div> <div class="translation abstracttxt"> <span class="zhankaihshouqi fivelineshidden" id="abstract"> <span>机译：</span><Abstract XMLNS =“http://www.wiley.com/namespaces/wiley”type =“main”xml：lang =“en”> <title type =“main”>摘要</ title> >细菌有被认为只在发酵葡萄糖或其他己糖时遵循一些公认的生化途径。这些途径已经在教科书的石头上凿了几十年，大多数来源渲染它们，因为它们出现在Gottschalk的经典1986年文本中。仍然尚不清楚这些途径如何适用，鉴于它们只有少数模型生物建立和划定生物化学。在这里，我们表明，公认的途径通常无法解释细菌形成的发酵产品。在对其种类的最广泛的分析中，我们从48种和细菌的亚种来自一个环境（瘤胃）的基因组的葡萄糖发酵的途径重建。总共有44％的细菌具有非典型途径，包括对细菌或任何生物完全前所未有的几种途径。详细中，8％的细菌具有乙酸盐形成的非典型途径; 21％的细菌具有非典型途径，用于丙酸盐或琥珀酸盐形成; 6％的？细菌对丁酸盐形成的非典型途径，33％的细菌具有非典型或不完全的Embden-Meyerhof-Parnas途径。本研究表明，如果使用良好识别的途径参考，则omics研究的共同目标 - 可能是不正确的。此外，它要求再次努力描绘发酵途径生物化学。</ p> </摘要> </span> <span class="z_kbtn z_kbtnclass hoverxs" style="display: none;">展开▼</span> </div> </div> <div class="record"> <h2 class="all_title" id="enpatent33" > 著录项</h2> <ul> <li> <span class="lefttit">来源</span> <div style="width: 86%;vertical-align: text-top;display: inline-block;"> <a href='/journal-foreign-22868/'>《Environmental microbiology 》</a> <b style="margin: 0 2px;">|</b><span>2017年第11期</span><b style="margin: 0 2px;">|</b> <span>共14页</span> </div> </li> <li> <div class="author"> <span class="lefttit">作者</span> <p id="fAuthorthree" class="threelineshidden zhankaihshouqi"> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Hackmann Timothy J.&option=202" target="_blank" rel="nofollow">Hackmann Timothy J.;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Ngugi David Kamanda&option=202" target="_blank" rel="nofollow">Ngugi David Kamanda;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Firkins Jeffrey L.&option=202" target="_blank" rel="nofollow">Firkins Jeffrey L.;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Tao Junyi&option=202" target="_blank" rel="nofollow">Tao Junyi;</a> </p> <span class="z_kbtnclass z_kbtnclassall hoverxs" id="zkzz" style="display: none;">展开▼</span> </div> </li> <li> <div style="display: flex;"> <span class="lefttit">作者单位</span> <div style="position: relative;margin-left: 3px;max-width: 639px;"> <div class="threelineshidden zhankaihshouqi" id="fOrgthree"> <p>Department of Animal ScienceUniversity of Florida P.O. Box 110910Gainesville FL 32611 USA;</p> <p>Red Sea Research CenterKing Abdullah University of Science and Technology (KAUST)Thuwal 23955‐6900 Saudi Arabia;</p> <p>Department of Animal ScienceThe Ohio State University 2029 Fyffe RdColumbus OH 43210 USA;</p> <p>Department of Animal ScienceUniversity of Florida P.O. Box 110910Gainesville FL 32611 USA;</p> </div> <span class="z_kbtnclass z_kbtnclassall hoverxs" id="zhdw" style="display: none;">展开▼</span> </div> </div> </li> <li> <span class="lefttit">收录信息</span> <span style="width: 86%;vertical-align: text-top;display: inline-block;"></span> </li> <li> <span class="lefttit">原文格式</span> <span>PDF</span> </li> <li> <span class="lefttit">正文语种</span> <span>eng</span> </li> <li> <span class="lefttit">中图分类</span> <span> <a href="https://www.zhangqiaokeyan.com/clc/183.html" title="微生物学">微生物学 ;</a></span> </li> <li class="antistop"> <span class="lefttit">关键词</span> <p style="width: 86%;vertical-align: text-top;"> </p> </li> </ul> </div> </div> <div class="literature cardcommon"> <div class="similarity "> <h3 class="all_title" id="enpatent66">相似文献</h3> <div class="similaritytab clearfix"> <ul> <li class="active" >外文文献</li> <li >中文文献</li> <li >专利</li> </ul> </div> <div class="similarity_details"> <ul > <li> <div> <b>1. </b><a class="enjiyixqcontent" href="/journal-foreign-detail/0704023229177.html">Genomes of rumen bacteria encode atypical pathways for fermenting hexoses to short‐chain fatty acids</a> <b>[J]</b> . <span> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Hackmann Timothy J.&option=202" target="_blank" rel="nofollow" class="tuijian_auth tuijian_authcolor">Hackmann Timothy J.,</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Ngugi David Kamanda&option=202" target="_blank" rel="nofollow" class="tuijian_auth tuijian_authcolor">Ngugi David Kamanda,</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Firkins Jeffrey L.&option=202" target="_blank" rel="nofollow" class="tuijian_auth tuijian_authcolor">Firkins Jeffrey L.,</a> <a href="/journal-foreign-22868/" target="_blank" rel="nofollow" class="tuijian_authcolor">Environmental microbiology .</a> <span>2017</span> <span>,第11期</span> </span> </div> <p class="zwjiyix translation" style="max-width: initial;height: auto;word-break: break-all;white-space: initial;text-overflow: initial;overflow: initial;"> <span>机译：瘤胃细菌的基因组编码非典型途径，用于发酵到短链脂肪酸中的己糖</span> </p> </li> <li> <div> <b>2. </b><a class="enjiyixqcontent" href="/academic-journal-foreign_journal-food-science_thesis/0204113769137.html">Effects of Lactic Acid Bacteria-Fermented Soymilk on Isoflavone Metabolites and Short-Chain Fatty Acids Excretion and Their Modulating Effects on Gut Microbiota</a> <b>[J]</b> . <span> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=&option=202" target="_blank" rel="nofollow" class="tuijian_auth tuijian_authcolor"> </a> <a href="/journal-foreign-2372/" target="_blank" rel="nofollow" class="tuijian_authcolor">Journal of Food Science .</a> <span>2019</span> <span>,第7a9期</span> </span> </div> <p class="zwjiyix translation" style="max-width: initial;height: auto;word-break: break-all;white-space: initial;text-overflow: initial;overflow: initial;"> <span>机译：乳酸菌发酵豆浆对异黄酮代谢产物和短链脂肪酸排泄的影响及其对肠道菌群的调节作用</span> </p> </li> <li> <div> <b>3. </b><a class="enjiyixqcontent" href="/academic-journal-foreign_detail_thesis/0204119082944.html">The metabolism of short-chain fatty acids in the sheep. 4. 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<b>7. </b><a class="enjiyixqcontent" href="/academic-degree-domestic_mphd_thesis/020313063134.html">日粮营养水平对山羊瘤胃、瓣胃上皮生长及短链脂肪酸浓度的影响</a> <b>[A] </b> <span> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=曾球生&option=202" target="_blank" rel="nofollow" class="tuijian_auth tuijian_authcolor"> . 曾球生</a> <span> . 2006</span> </span> </div> </li> </ul> <ul style="display: none;"> <li> <div> <b>1. </b><a class="enjiyixqcontent" href="/patent-detail/06120110858318.html">短链脂肪酸及利用污泥厌氧发酵生成短链脂肪酸的方法</a> <b>[P]</b> . <span> 中国专利： CN108384816A </span> <span> . 2018-08-10</span> </div> </li> <li> <div> <b>2. </b><a class="enjiyixqcontent" href="/patent-detail/061203404708.html">一种赤泥联合瘤胃液处理污泥促进短链脂肪酸生成的方法</a> <b>[P]</b> . <span> 中国专利： CN106865937B </span> <span> . 2019.07.26</span> </div> </li> <li> <div> <b>3. </b><a class="enjiyixqcontent" href="/patent-detail/06130501069647.html">GROUP OF MICROORGANISMS FORMED BY LACTOBACILLUS SP. STRAIN K03D08, BACILLUS SP. STRAIN K03B01 AND KAZACHSTANIA SP. STRAIN K03K02G AND COMPOSITIONS THEREOF; METHOD FOR OBTAINING A CASEIN-FREE DAIRY BYPRODUCT CONTAINING SHORT-CHAIN FATTY ACIDS AND HYDROXYLATED SHORT-CHAIN FATTY ACIDS GENERATED BY THE METABOLISM OF THE GROUP OF MICROORGANISMS</a> <b>[P]</b> . <span> 外国专利：  WO2021171061A1 </span> <span> . 2021-09-02</span> </div> <p class="zwjiyix translation" style="max-width: initial;height: auto;word-break: break-all;white-space: initial;text-overflow: initial;overflow: initial;"> <span>机译：由乳酸杆菌组成的微生物组。菌株K03D08，芽孢杆菌SP。菌株K03b01和Kazachstania sp。菌株K03K02G及其组合物; 获得含有短链脂肪酸和通过微生物组代谢产生的短链脂肪酸和羟基化短链脂肪酸的酪蛋白的乳制品副产物的方法 </span> </p> </li> <li> <div> <b>4. </b><a class="enjiyixqcontent" href="/patent-detail/06130420195388.html">pharmaceuticals and / or dietary compositions based on short chain fatty acids. pharmaceutical compositions and / or diet based on short chain fatty acids.</a> <b>[P]</b> . <span> 外国专利：  IT1401309B1 </span> <span> . 2013-07-18</span> </div> <p class="zwjiyix translation" style="max-width: initial;height: auto;word-break: break-all;white-space: initial;text-overflow: initial;overflow: initial;"> <span>机译：基于短链脂肪酸的药物和/或饮食组合物。药物组合物和/或基于短链脂肪酸的饮食。 </span> </p> </li> <li> <div> <b>5. </b><a class="enjiyixqcontent" href="/patent-detail/06130422782153.html">pharmaceuticals and / or dietary compositions based on short chain fatty acids.composizioni pharmaceutical and / or diet based on short chain fatty acids.</a> <b>[P]</b> . <span> 外国专利：  ITMI20101477A1 </span> <span> . 2012-02-04</span> </div> <p class="zwjiyix translation" style="max-width: initial;height: auto;word-break: break-all;white-space: initial;text-overflow: initial;overflow: initial;"> <span>机译：基于短链脂肪酸的药物和/或饮食组合物。composizioni基于短链脂肪酸的药物和/或饮食组合。 </span> </p> </li> </ul> </div> </div> </div> <div class="theme cardcommon" style="overflow: auto;display:none"> <h3 class="all_title" id="enpatent55">相关主题</h3> <ul id="subject"> </ul> </div> </div> </div> </div> <div class="right rightcon"> <div class="details_img cardcommon 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